Man pages for eMetaboHUB/MS-CleanR
Cleans MS Data for Easier Analyses
| annotate_cluster | Annotate a single cluster |
| check_architecture_for_clean_msdial_data | Check project architecture before running... |
| check_architecture_for_keep_top_peaks | Check project architecture before running 'keep_top_peaks'. |
| check_architecture_for_launch_msfinder_annotation | Check project architecture before running... |
| check_boolean | Check if value is boolean. |
| check_for_convert_csv_to_msp | Check before running 'launch_msfinder_annotation'. |
| check_input_parameters_keep_top_peaks | Check if input parameters are correct before running... |
| check_input_parameters_launch_msfinder | Check if input parameters are correct before running... |
| check_input_parameters_msdial_data | Check if input parameters are correct before running... |
| check_main_architecture | Check the project main architecture |
| check_path | Check if a path exist. |
| check_positive_int | Check if value is a positive integer. |
| check_positive_num | Check if value is a positive numerical value. |
| check_probability | Check if value is a probability (numerical value between 0... |
| check_references | Check if value is a correct reference data.frame |
| choose_project_directory | Declare the project directory for the analysis process. |
| clean_for_current_run | Create a directory or delete a file for a new run. |
| clean_msc_combinations | Cleans the columns name of data generated my MSCombine. |
| clean_msdial_data | Combine pos and neg files from MSDial and filter peaks... |
| clear_duplicate_links | Clear duplicate undirected MSDial links. |
| compute_massdiff | Compute mass differences between 2 lists of adducts |
| concat_msp_files | Concatenate all MSP files present in the folder at 'path'. |
| convert_csv_to_msp | Convert the final CSV file post annotations to MSP format. |
| detect_posneg_combinations | Detect possible adducts, neutral losses and positive and... |
| detect_single_polarity_combinations | Detect possible adducts and neutral losses. |
| export_data | Export data for users. |
| extract_concatenated_data_from_column | Extract data concatenated in a single column. |
| extract_msdial_links | Extract links between elements identified by MSDial. |
| find_structure | Find the most probable structure by iterating over all... |
| get_adducts_nl_links | Detect possible neutral losses, isotopes and adduct links. |
| get_confirmation_for_overwriting | Ask the user confirmation for overwriting if the path already... |
| get_most_probable | Get the most probable structure for the whole input... |
| get_pattern_file | Get path for a file found thanks to a pattern. |
| get_project_file_path | Get path for a project file or directory. |
| get_samples_info | Get samples names and class from an MSDial file and generate... |
| import_data | Import data exported by the script. |
| import_msdial_data | Import all data generated by MSDial. |
| import_msdial_file | Import an MS file generated by MSDial. |
| import_msfinder_base_file | Generic function for importing a file generated by MSFinder |
| import_msfinder_data | Import files generated by MSFinder, both formula and... |
| import_msfinder_formula_file | Import a formula file generated by MSFinder. |
| import_msfinder_structure_file | Import a structure file generated by MSFinder. |
| increment_strings | Increment the final number in strings. |
| keep_top_peaks | Filter peaks based on a given criterion. |
| launch_msfinder_annotation | Annotates peaks based on files extracted from MSFinder. |
| mass_adducts_neg | Mass differences of adducts with the original compound M, in... |
| mass_adducts_pos | Mass differences of adducts with the original compound M, in... |
| mass_isotopes | Masses of isotopes. |
| mass_neutral_loss_neg | Masses of neutral losses, in negative mode. |
| mass_neutral_loss_pos | Masses of neutral losses, in positive mode. |
| matrix_to_df | Transform a matrix to a data.frame. |
| mscleanr | mscleanr: A package for cleaning and analyzing MS data |
| print_message | Print a message in green. |
| print_peaks_status | Print number of peaks in data in a message for the user. |
| print_warning | Print a warning in yellow. |
| recurrent_params | Return documentation info for recurrent parameters. |
| runGUI | Launch the Graphical User Interface (GUI) |
| stop_script | Stop the script after printing an error. |
| substrRight | Extract characters from a string from the right. |
| update_annotations_scores | Adapt the final annotations scores. |
